Interaction between DNA ligase 1 (6q1v_A) and DNA (6q1v_D_B_C)

PDB and SCOP data

PDB ID: 6q1v (all binary interactions in this PDB entry)

Title: Human DNA Ligase 1 (E592R) Bound to an Adenylated, hydroxyl terminated DNA nick

Release date: 2019-12-11

Resolution: 1.9 Å

  • Chain A: 6q1v_A

    Title: DNA ligase 1

    Source organism: Homo sapiens

    Number of residues: 645 (3 missing in structure)

  • Chain B: 6q1v_D_B_C

    Title: DNA

    Source organism: synthetic construct

    Number of residues: 36

    Note: Residues of nucleic acid domain are renumbered to avoid repeating the same residue numbers from different PDB chains.

Buried interface area: 2431.32 Å2

Number of inter-residue contacts at the interface: 200

Number of H-bonds: 36

  • Pairwise interaction

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    Download PyMOL visualization script

  • Biological assembly

    Homomer, 1 protein, 1 nucleic acid.

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Create a structural model for this interaction

  • Interface residues in 6q1v_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 303 44 S 41.8 38.8 %
    2 304 45 A 25.2 44.5 %
    3 305 46 R 52.4 42.9 %
    4 306 47 L 4.7 3.3 %
    5 345 86 L 4.7 8.9 %
    6 346 87 E 52.3 41.9 %
    7 347 88 L 11.6 39.5 %
    8 348 89 G 29.4 56.5 %
    9 349 90 V 19.4 97.2 %
    10 350 91 G 28.5 78.3 %
    11 351 92 D 5.5 11.8 %
    12 352 93 G 23.4 54.1 %
    13 353 94 V 19.7 53.8 %
    14 356 97 K 17.0 16.9 %
    15 370 111 R 6.1 6.1 %
    16 414 155 L 0.9 2.0 %
    17 415 156 T 14.5 11.9 %
    18 416 157 G 27.5 52.0 %
    19 417 158 S 15.9 13.8 %
    20 418 159 A 18.3 25.8 %
    21 419 160 S 17.4 93.5 %
    22 420 161 T 37.5 56.4 %
    23 421 162 A 1.1 1.7 %
    24 423 164 K 2.7 14.2 %
    25 447 188 S 0.7 3.8 %
    26 449 190 R 34.3 31.2 %
    27 451 192 R 47.3 47.8 %
    28 452 193 L 5.9 47.3 %
    29 453 194 G 35.5 64.3 %
    30 454 195 L 14.2 75.7 %
    31 455 196 A 39.4 59.7 %
    32 456 197 E 4.7 11.1 %
    33 457 198 Q 51.8 54.9 %
    34 458 199 S 13.0 100.0 %
    35 504 245 K 12.0 20.5 %
    36 546 287 H 27.1 40.6 %
    37 547 288 P 9.2 16.3 %
    38 549 290 R 26.6 20.5 %
    39 557 298 R 32.9 40.1 %
    40 568 309 K 8.8 97.9 %
    41 570 311 D 3.2 14.5 %
    42 571 312 G 12.7 99.7 %
    43 572 313 Q 31.1 80.3 %
    44 573 314 R 13.4 83.5 %
    45 588 329 S 21.0 91.2 %
    46 589 330 R 43.7 46.0 %
    47 590 331 N 31.2 36.3 %
    48 592 333 R 54.8 47.2 %
    49 594 335 N 4.0 17.7 %
    50 597 338 K 5.7 24.8 %
    51 621 362 E 4.3 88.9 %
    52 635 376 F 40.2 69.2 %
    53 636 377 Q 35.9 50.2 %
    54 639 380 T 46.2 64.3 %
    55 640 381 T 39.9 44.0 %
    56 641 382 R 9.0 41.9 %
    57 642 383 K 44.7 29.5 %
    58 643 384 R 96.2 59.4 %
    59 644 385 K 52.5 32.2 %
    60 720 461 E 9.0 28.7 %
    61 737 478 K 3.0 2.1 %
    62 738 479 R 43.5 35.4 %
    63 739 480 S 16.3 40.3 %
    64 740 481 H 12.9 17.8 %
    65 744 485 K 19.6 72.1 %
    66 746 487 K 18.1 86.9 %
    67 748 489 D 1.8 10.7 %
    68 749 490 Y 28.6 95.6 %
    69 765 506 Y 3.6 13.2 %
    70 766 507 L 2.7 5.7 %
    71 767 508 G 3.9 82.2 %
    72 768 509 R 30.1 34.9 %
    73 769 510 G 9.2 49.7 %
    74 770 511 K 82.3 45.6 %
    75 771 512 R 38.2 57.5 %
    76 776 517 G 19.0 98.4 %
    77 777 518 G 11.4 87.9 %
    78 778 519 F <0.1 99.6 %
    79 794 535 C 9.2 100.0 %
    80 795 536 K 62.3 69.0 %
    81 796 537 L 9.1 100.0 %
    82 797 538 G 35.0 99.5 %
    83 798 539 T 59.2 92.0 %
    84 799 540 G 34.6 89.0 %
    85 800 541 F 12.1 89.9 %
    86 801 542 S 29.3 52.1 %
    87 802 543 D 41.7 39.2 %
    88 803 544 E 1.9 1.4 %
    89 804 545 E 0.5 0.9 %
    90 845 586 K 0.5 4.5 %
    91 850 591 S 23.1 71.1 %
    92 851 592 L 8.9 21.4 %
    93 852 593 S 14.1 98.6 %
    94 853 594 P 35.0 36.0 %
    95 854 595 I 11.2 18.7 %
    96 855 596 Y 23.8 93.1 %
    97 866 607 K 11.3 13.3 %
    98 869 610 S 19.3 100.0 %
    99 870 611 L 13.2 100.0 %
    100 871 612 R 23.7 49.0 %
    101 872 613 F 86.7 96.9 %
    102 873 614 P 29.5 95.1 %
    103 874 615 R 48.0 99.7 %
    104 875 616 F 0.2 4.5 %
    105 876 617 I 4.5 6.2 %

  • Interface residues in 6q1v_D_B_C

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 1 9:D1 G 51.6 22.5 %
    2 2 10:D1 T 70.2 42.5 %
    3 3 11:D1 C 102.5 60.0 %
    4 4 12:D1 C 93.6 62.5 %
    5 5 13:D1 G 98.0 52.3 %
    6 6 14:D1 A 142.8 87.9 %
    7 7 15:D1 C 106.0 63.8 %
    8 8 16:D1 G 116.0 64.8 %
    9 9 17:D1 A 102.6 71.1 %
    10 10 18:D1 C 91.4 73.9 %
    11 11 19:D1 G 107.9 73.7 %
    12 12 20:D1 C 91.7 55.9 %
    13 13 21:D1 A 84.5 57.3 %
    14 14 22:D1 T 17.9 9.3 %
    15 15 23:D1 C 75.3 44.4 %
    16 16 24:D1 A 61.3 42.6 %
    17 17 25:D1 G 16.2 9.1 %
    18 24 8:B1 T 22.9 12.6 %
    19 25 9:B1 G 91.6 59.0 %
    20 26 10:B1 C 74.0 47.5 %
    21 27 11:B1 G 86.6 48.9 %
    22 28 12:B1 T 109.5 66.4 %
    23 29 13:B1 C 129.7 84.8 %
    24 30 1:C1 G 73.9 62.1 %
    25 31 2:C1 T 114.2 75.6 %
    26 32 3:C1 C 105.2 66.8 %
    27 33 4:C1 G 64.0 33.4 %
    28 34 5:C1 G 51.3 29.9 %
    29 35 6:C1 A 21.7 12.1 %
    30 36 7:C1 C 57.0 20.3 %

No. Residue no. in chain A structure Residue no. in chain A sequence Residue in chain A Residue no. in chain B structure Residue no. of chain B in PDB Residue in chain B Contact area, Å2 Contact type
1 303 44 S 35 6:C1 A 21.4
2 303 44 S 36 7:C1 C 20.4 H-bond
3 304 45 A 36 7:C1 C 25.2
4 305 46 R 2 10:D1 T 1.3
5 305 46 R 3 11:D1 C 36.1
6 305 46 R 4 12:D1 C 8.3
7 305 46 R 36 7:C1 C 6.7
8 306 47 L 36 7:C1 C 4.7
9 345 86 L 27 11:B1 G 4.7
10 346 87 E 26 10:B1 C 30.4
11 346 87 E 27 11:B1 G 21.9
12 347 88 L 26 10:B1 C 11.6
13 348 89 G 25 9:B1 G 20.3
14 348 89 G 26 10:B1 C 9.1 H-bond
15 349 90 V 25 9:B1 G 5.2
16 349 90 V 26 10:B1 C 14.2
17 350 91 G 25 9:B1 G 24.4 H-bond
18 350 91 G 26 10:B1 C 4.1
19 351 92 D 25 9:B1 G 5.5
20 352 93 G 24 8:B1 T 11.1
21 352 93 G 25 9:B1 G 12.2
22 353 94 V 24 8:B1 T 5.6
23 353 94 V 25 9:B1 G 14.1 H-bond
24 356 97 K 16 24:D1 A 0.8
25 356 97 K 17 25:D1 G 16.2
26 370 111 R 24 8:B1 T 6.1
27 414 155 L 15 23:D1 C 0.9
28 415 156 T 15 23:D1 C 14.5
29 416 157 G 15 23:D1 C 27.2 H-bond
30 416 157 G 16 24:D1 A 0.4
31 417 158 S 15 23:D1 C 7.3
32 417 158 S 16 24:D1 A 8.6
33 418 159 A 16 24:D1 A 18.3 H-bond
34 419 160 S 15 23:D1 C 12.9
35 419 160 S 16 24:D1 A 4.6
36 420 161 T 15 23:D1 C 9.8
37 420 161 T 16 24:D1 A 27.7 H-bond
38 421 162 A 16 24:D1 A 1.1
39 423 164 K 15 23:D1 C 2.7
40 447 188 S 26 10:B1 C 0.7
41 449 190 R 6 14:D1 A 17.3
42 449 190 R 7 15:D1 C 17.0 H-bond
43 451 192 R 5 13:D1 G 19.7
44 451 192 R 6 14:D1 A 27.6
45 452 193 L 5 13:D1 G 5.9
46 453 194 G 4 12:D1 C 19.0
47 453 194 G 5 13:D1 G 16.5 H-bond
48 454 195 L 4 12:D1 C 5.7
49 454 195 L 5 13:D1 G 8.5
50 455 196 A 4 12:D1 C 25.9 H-bond
51 455 196 A 5 13:D1 G 13.5
52 456 197 E 4 12:D1 C 4.7
53 457 198 Q 3 11:D1 C 37.8
54 457 198 Q 4 12:D1 C 14.0 H-bond
55 458 199 S 3 11:D1 C 1.4
56 458 199 S 4 12:D1 C 11.6 H-bond
57 504 245 K 3 11:D1 C 12.0
58 546 287 H 1 9:D1 G 6.4
59 546 287 H 2 10:D1 T 20.7
60 547 288 P 31 2:C1 T 3.1
61 547 288 P 32 3:C1 C 6.1
62 549 290 R 32 3:C1 C 26.6 H-bond
63 557 298 R 1 9:D1 G 27.6
64 557 298 R 2 10:D1 T 5.3
65 568 309 K 29 13:B1 C <0.1
66 568 309 K 30 1:C1 G 8.8 H-bond
67 570 311 D 29 13:B1 C 3.2
68 571 312 G 29 13:B1 C 12.7
69 572 313 Q 28 12:B1 T 20.3
70 572 313 Q 29 13:B1 C 10.8
71 573 314 R 28 12:B1 T <0.1
72 573 314 R 29 13:B1 C 13.3 H-bond
73 588 329 S 28 12:B1 T 20.8 H-bond
74 588 329 S 29 13:B1 C 0.2
75 589 330 R 28 12:B1 T 0.7
76 589 330 R 29 13:B1 C 24.2
77 589 330 R 30 1:C1 G 18.8
78 590 331 N 28 12:B1 T 25.7 H-bond
79 590 331 N 29 13:B1 C 5.5
80 592 333 R 27 11:B1 G 43.7 H-bond
81 592 333 R 28 12:B1 T 11.1
82 594 335 N 28 12:B1 T 4.0
83 597 338 K 28 12:B1 T 5.7
84 621 362 E 29 13:B1 C 3.9
85 621 362 E 30 1:C1 G 0.3
86 635 376 F 9 17:D1 A 5.0
87 635 376 F 28 12:B1 T 16.3
88 635 376 F 29 13:B1 C 18.9
89 636 377 Q 10 18:D1 C 17.4
90 636 377 Q 11 19:D1 G 18.5 H-bond
91 639 380 T 10 18:D1 C 2.5
92 639 380 T 11 19:D1 G 28.7 H-bond
93 639 380 T 12 20:D1 C 7.7
94 639 380 T 27 11:B1 G 2.3
95 639 380 T 28 12:B1 T 5.0
96 640 381 T 11 19:D1 G 17.2
97 640 381 T 12 20:D1 C 22.7
98 641 382 R 12 20:D1 C 9.0
99 642 383 K 12 20:D1 C 22.3
100 642 383 K 13 21:D1 A 22.4
101 643 384 R 11 19:D1 G 10.7
102 643 384 R 12 20:D1 C 30.0
103 643 384 R 13 21:D1 A 27.5 H-bond
104 643 384 R 25 9:B1 G 9.9
105 643 384 R 26 10:B1 C 4.0
106 643 384 R 27 11:B1 G 14.1
107 644 385 K 13 21:D1 A 34.6
108 644 385 K 14 22:D1 T 17.9
109 720 461 E 29 13:B1 C 7.2
110 720 461 E 30 1:C1 G 1.8
111 737 478 K 2 10:D1 T 3.0
112 738 479 R 1 9:D1 G 17.6
113 738 479 R 2 10:D1 T 25.9 H-bond
114 739 480 S 2 10:D1 T 1.1
115 739 480 S 3 11:D1 C 15.3
116 740 481 H 2 10:D1 T 12.9
117 744 485 K 30 1:C1 G 2.7
118 744 485 K 31 2:C1 T 16.9 H-bond
119 746 487 K 30 1:C1 G 6.8
120 746 487 K 31 2:C1 T 11.4 H-bond
121 748 489 D 31 2:C1 T 1.7
122 748 489 D 32 3:C1 C <0.1
123 749 490 Y 31 2:C1 T 21.2 H-bond
124 749 490 Y 32 3:C1 C 7.4
125 765 506 Y 8 16:D1 G 3.6
126 766 507 L 7 15:D1 C 2.7
127 767 508 G 7 15:D1 C 3.9
128 768 509 R 6 14:D1 A 9.0 H-bond
129 768 509 R 7 15:D1 C 21.1 H-bond
130 769 510 G 6 14:D1 A 9.2
131 770 511 K 4 12:D1 C 4.3
132 770 511 K 5 13:D1 G 33.2 H-bond
133 770 511 K 6 14:D1 A 34.6 H-bond
134 770 511 K 33 4:C1 G 10.0
135 770 511 K 34 5:C1 G 0.1
136 771 512 R 5 13:D1 G 0.7
137 771 512 R 6 14:D1 A 31.3
138 771 512 R 7 15:D1 C 3.6
139 771 512 R 33 4:C1 G 2.6
140 776 517 G 6 14:D1 A <0.1
141 776 517 G 7 15:D1 C 19.0
142 777 518 G 7 15:D1 C 7.4
143 777 518 G 8 16:D1 G 4.0
144 778 519 F 8 16:D1 G <0.1
145 794 535 C 8 16:D1 G 0.5
146 794 535 C 9 17:D1 A 8.7
147 795 536 K 8 16:D1 G 41.7 H-bond
148 795 536 K 9 17:D1 A 20.6 H-bond
149 796 537 L 7 15:D1 C 0.4
150 796 537 L 8 16:D1 G 8.7
151 797 538 G 6 14:D1 A 5.0
152 797 538 G 7 15:D1 C 22.8
153 797 538 G 8 16:D1 G 7.2
154 798 539 T 6 14:D1 A 8.7
155 798 539 T 7 15:D1 C 8.1
156 798 539 T 8 16:D1 G 3.1
157 798 539 T 30 1:C1 G 5.2
158 798 539 T 31 2:C1 T 17.2
159 798 539 T 32 3:C1 C 16.8
160 799 540 G 32 3:C1 C 17.1
161 799 540 G 33 4:C1 G 17.5
162 800 541 F 33 4:C1 G 12.1
163 801 542 S 33 4:C1 G 17.7
164 801 542 S 34 5:C1 G 11.6
165 802 543 D 33 4:C1 G 3.7
166 802 543 D 34 5:C1 G 37.7 H-bond
167 802 543 D 35 6:C1 A 0.3
168 803 544 E 34 5:C1 G 1.9
169 804 545 E 33 4:C1 G 0.5
170 845 586 K 32 3:C1 C 0.5
171 850 591 S 9 17:D1 A 6.0
172 850 591 S 10 18:D1 C 17.1 H-bond
173 851 592 L 10 18:D1 C 5.9
174 851 592 L 11 19:D1 G 2.9
175 852 593 S 10 18:D1 C 14.1 H-bond
176 853 594 P 10 18:D1 C 16.3
177 853 594 P 11 19:D1 G 18.6
178 854 595 I 9 17:D1 A 3.9
179 854 595 I 10 18:D1 C 7.3
180 855 596 Y 9 17:D1 A 19.8 H-bond
181 855 596 Y 10 18:D1 C 4.0
182 866 607 K 11 19:D1 G 11.3
183 869 610 S 9 17:D1 A 12.6
184 869 610 S 10 18:D1 C 6.7
185 870 611 L 9 17:D1 A 13.2
186 871 612 R 8 16:D1 G 2.8
187 871 612 R 9 17:D1 A 6.3
188 871 612 R 29 13:B1 C 14.6
189 872 613 F 8 16:D1 G 20.9
190 872 613 F 9 17:D1 A 1.6
191 872 613 F 29 13:B1 C 15.0
192 872 613 F 30 1:C1 G 29.5
193 872 613 F 31 2:C1 T 19.7
194 873 614 P 8 16:D1 G 23.4
195 873 614 P 9 17:D1 A 5.0
196 873 614 P 31 2:C1 T 1.1
197 874 615 R 31 2:C1 T 22.0
198 874 615 R 32 3:C1 C 26.0 H-bond
199 875 616 F 32 3:C1 C 0.2
200 876 617 I 32 3:C1 C 4.5

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
B6q1v_D_B_C101TRS 105.926.3
B6q1v_D_B_C101AMP 45.0307.3

  • Query protein: sp|P49916|DNLI3_HUMAN DNA ligase 3 OS=Homo sapiens GN=LIG3 PE=1 SV=2

    Result domain: 6q1v_A; DNA ligase 1

    Alignment data:

    Expectation value = 3.90e-48, Score = 186 bits (470),

    Identities = 33% (124/373), Positive = 50% (188/373), Gaps = 9% (35/373).

    Interface alignment data:

    Interface residues in alignment: 67% (70/105).

    Identities = 41% (29/70), Positive = 57% (40/70), Gaps = 4% (3/70).

    Query: 480 PVQPMLAEACKSVEYAMKKCPNGMFS-EIKYDGERVQVHK-NGDHFSYFSRSLKPVLPHK 537

    P++PMLA + + +K+ F+ E KYDG+R Q+H G FSR+ +

    6q1v_A: 280 PLKPMLAHPTRGISEVLKRFEEAAFTCEYKYDGQRAQIHALEGGEVKIFSRNQR----DN 335

    dssp: ------EEE---HHHHHHHH----EEEEE----EEEEEEE-----EEEE----- E-


    Query: 538 VAHFKDYIPQA----FPGGHSMILDSEVLLIDNKTGKPLPFGTLGVHKK----AAFQDAN 589

    + D I + P S ILD+E + D + + PF L K+ A+

    6q1v_A: 336 TGKYPDIISRIPKIKLPSVTSFILDTEAVAWDREKKQIQPFQVLTTRKRKEVDASEIQVQ 395

    dssp: HHH-HHHHH-HHHHE------EEEEEEEEEEE----EE--HHHH---------HHH----


    Query: 590 VCLFVFDCIYFNDVSLMDRPLCERRKFLHDNMVEIPNRIMFSEMKRVTKALDLADMITRV 649

    VCL+ FD IY N SL+ PL RR+ L +N VE +F+ +A+ + +

    6q1v_A: 396 VCLYAFDLIYLNGESLVREPLSRRRQLLRENFVETEGEFVFATSLDTKDIEQIAEFLEQS 455

    dssp: EEEEEEEEEEE--EE-----HHHHHHHHHHHE--E---EEE--EEE---HHHHHHHHHHH


    Query: 650 IQEGLEGLVLK--DVKGTYEPGKR--HWLKVKKDYLNEGAMADTADLVVLGAFYGQGSKG 705

    +++ EGL++K DV TYE KR +WLK+KKDYL+ + DT DLVV+GA+ G+G +

    6q1v_A: 456 VKDSCEGLMVKTLDVDATYEIAKRSHNWLKLKKDYLD--GVGDTLDLVVIGAYLGRGKRA 513

    dssp: HH----EEEEEE---------------EEEEEHHH-- ---EEEEEEEEEEEE--HHH-


    Query: 706 GMMSIFLMGCYDPGSQKWCTVTKCAGGHDDATLARLQNELDMVKISKDPSKIPSWLKVNK 765

    G FL+ YD S++ + K G D L L + + PS P +++++

    6q1v_A: 514 GRYGGFLLASYDEDSEELQAICKLGTGFSDEELEEHHQSLKALVL---PSPRP-YVRIDG 569

    dssp: --EEEEEEEEEE----EEEEEEEE-----HHHHHHHHHHHHHHEE ----- -EE---


    Query: 766 IYYPDFIVPDPKKAAVWEITGAEFSKSEAHTA--------DGISIRFPRCTRIRDDKDWK 817

    PD + DP +AVWE+ A+ S S + A GIS+RFPR R+R+DK +

    6q1v_A: 570 AVIPDHWL-DP--SAVWEVKCADLSLSPIYPAARGLVDSDKGISLRFPRFIRVREDKQPE 626

    dssp: -----EEE -- --EEEEEE-EEEEE--------------EEEEE--EEEEE-----HH


    Query: 818 SATNLPQLKELYQ 830

    AT Q+ LY+

    6q1v_A: 627 QATTSAQVACLYR 639

    dssp: H--EHHHHHHHHH


    Download alignment FASTA file